Dynamic Dictionary Matching in External Memory

In thedynamic dictionary matchingproblem, a dictionaryDcontains a set of patterns that can change over time under insertion and deletion of individual patterns. Given an arbitrary textT, we must efficiently list all the dictionary patterns that occur at each text position. We investigate the I/O complexity of this problem for a large dictionary that must be stored in external storage devices. By following a completely new approach, we devise an efficient solution which is based upon the SB-tree data structure (P. Ferragina and R. Grossi, 1995,in“Proc. ACM Symposium on Theory of Computing,” pp. 693–702), and a novel notion of certificate for the dictionary matching problem. Our data structure can be adapted to efficiently work in main memory and to solve other problems, thus providing a new insight into the nature of the dictionary matching problem.     

A Theoretical and Experimental Study on the Construction of Suffix Arrays in External Memory

The construction of full-text indexes on very large text collections is nowadays a hot problem. The suffix array [32] is one of the most attractive full-text indexing data structures due to its simplicity, space efficiency and powerful/ fast search operations supported. In this paper we analyze, both theoretically and experimentally, the I/ O complexity and the working space of six algorithms for constructing large suffix arrays. Three of them are state-of-the-art, the other three algorithms are our new proposals. We perform a set of experiments based on three different data sets (English texts, amino-acid sequences and random texts) and give a precise hierarchy of these algorithms according to their working-space versus construction-time tradeoff. Given the current trends in model design [12], [32] and disk technology [29], [30], we pose particular attention to differentiate between ``random'' and ``contiguous'' disk accesses, in order to explain reasonably some practical I/ O phenomena which are related to the experimental behavior of these algorithms and that would otherwise be meaningless in the light of other simpler external-memory models. We also address two other issues. The former is concerned with the problem of building word indexes; we show that our results can be successfully applied to this case too, without any loss in efficiency and without compromising the simplicity of programming to achieve a uniform, simple and efficient approach to both the two indexing models. The latter issue is related to the intriguing and apparently counterintuitive ``contradiction'' between the effective practical performance of the well-known Baeza-Yates—Gonnet—Snider algorithm [17], verified in our experiments, and its unappealing worst-case behavior. We devise a new external-memory algorithm that follows the basic philosophy underlying that algorithm but in a significantly different manner, thus resulting in a novel approach which combines good worst-case bounds with efficient practical performance.     

Titanium phosphate surfactants intercalation compounds: Thermal and structural characterization

Titanium phosphate containing long chain surfactants can be synthesized either by batch using the inorganic ion-exchanger γ-titanium phosphate and surfactant solutions or via sol-gel by direct intercalation. The resulting content of the surfactants after being exchanged depends on the length of the chain and is greater in the case of the material obtained by direct intercalation. All of the material obtained has a layered structure and an increased interlayer distance. The longer the chain is the greater the increase in distance. The layered structure is maintained up to 300 °C. The pyrophosphate formation occurs at 900 °C in the case of material by direct intercalation, whereas in the case of batch material it occurs at a higher temperature. The surfactant loss occurs in three or more distinct stages. As far as the batch material is concerned the last loss occurs at a high temperature of ∼800 °C. Thermal treatment is carried out in air or nitrogen atmosphere for the better characterization of the processes.     

Recognition by constructive neural algorithms

The usability of the constructive neural algorithms as pattern classifiers is investigated. It is pointed out that the unboundedness of the decision regions formed by most neural recognizers leads to substantial limitations of the generalization capabilities of these nets. We specify a constructive neural recognizer that forms bounded decision regions, and report the results of this algorithm on a series of benchmark problems that resemble the usual pattern recognition problems.     

The use of Fourier-transform infrared spectroscopy to predict cheese yield and nutrient recovery or whey loss traits from unprocessed bovine milk samples

Cheese yield is an important technological trait in the dairy industry in many countries. The aim of this study was to evaluate the effectiveness of Fourier-transform infrared (FTIR) spectral analysis of fresh unprocessed milk samples for predicting cheese yield and nutrient recovery traits. A total of 1,264 model cheeses were obtained from 1,500-mL milk samples collected from individual Brown Swiss cows. Individual measurements of 7 new cheese yield-related traits were obtained from the laboratory cheese-making procedure, including the fresh cheese yield, total solid cheese yield, and the water retained in curd, all as a percentage of the processed milk, and nutrient recovery (fat, protein, total solids, and energy) in the curd as a percentage of the same nutrient contained in the milk. All individual milk samples were analyzed using a MilkoScan FT6000 over the spectral range from 5,000 to 900 wavenumber × cm⁻¹. Two spectral acquisitions were carried out for each sample and the results were averaged before data analysis. Different chemometric models were fitted and compared with the aim of improving the accuracy of the calibration equations for predicting these traits. The most accurate predictions were obtained for total solid cheese yield and fresh cheese yield, which exhibited coefficients of determination between the predicted and measured values in cross-validation (1-VR) of 0.95 and 0.83, respectively. A less favorable result was obtained for water retained in curd (1-VR = 0.65). Promising results were obtained for recovered protein (1-VR = 0.81), total solids (1-VR = 0.86), and energy (1-VR = 0.76), whereas recovered fat exhibited a low accuracy (1-VR = 0.41). As FTIR spectroscopy is a rapid, cheap, high-throughput technique that is already used to collect standard milk recording data, these FTIR calibrations for cheese yield and nutrient recovery highlight additional potential applications of the technique in the dairy industry, especially for monitoring cheese-making processes and milk payment systems. In addition, the prediction models can be used to provide breeding organizations with information on new phenotypes for cheese yield and milk nutrient recovery, potentially allowing these traits to be enhanced through selection.     

Foreword

This special issue contains selected papers from FUN with Algorithms 2004, the third conference dedicated to the design, analysis, and use of algorithms and data structures that provide amusing, witty, but nonetheless original and scientifically profound contributions to the area.     

Intercalation of Ru(II) tris (1,10-phenanthroline) complex in α- and γ-zirconium dihydrogen phosphate. Synthesis, thermal behaviour and X-ray characterization

Layered inorganic systems such as ion-exchangers (α- and γ-zirconium dihydrogen phosphate) already used as hosts for larger cations, were studied for the intercalation of Ru(II) tris (1,10-phenanthroline) complex into these host matrices. The uptake of the complex occurs using the batch method; the colour of the materials changes from white to brilliant orange; the highest ion uptake is obtained in the case of the γ-phase. The materials obtained are thermally stable up to ∼350 °C and the complex decomposition occurs in two (α-phase) or three (γ-phase) steps. The complex decomposition is complete at ∼700 °C and at 550 °C (respectively for α- and γ-Ru(II) materials). As can be seen from the X-ray patterns, the Ru(II) materials are still layered and show a new phase with an increase in the interlayer distance with respect to the starting materials. The hydrogen form is always present in the case of the α-materials; whereas, in the case of the γ-materials, it is present when ≤0.12 moles of the complex/mole of exchanger are inserted. Microanalysis measurements confirm the fact that the Ru(II) complex is not modified when exchanged.     

Use of rapid prototyping models in the planning of percutaneous pulmonary valved stent implantation

Percutaneous replacement of the pulmonary valve is a recently developed interventional technique which involves the implantation of a valved stent in the pulmonary trunk. It relies upon careful consideration of patient anatomy for both stent design and detailed procedure planning. Medical imaging data in the form of two-dimensional scans and three-dimensional interactive graphics offer only limited support for these tasks. The paper reports the results of an experimental investigation on the use of arterial models built by rapid prototyping techniques. An analysis of clinical needs has helped to specify proper requirements for such model properties as cost, strength, accuracy, elastic compliance, and optical transparency. Two different process chains, based on the fused deposition modelling technique and on the vacuum casting of thermoset resins in rubber moulds, have been tested for prototype fabrication. The use of anatomical models has allowed the cardiologist's confidence in patient selection, prosthesis fabrication, and final implantation to be significantly improved.